Contacts of the strand formed by residues 204 - 207 (chain G) in PDB entry 6PSU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 204 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23G HIS* 3.0 38.4 + - + +
25G LYS* 3.9 23.0 - - + +
182G ARG* 3.5 27.5 + - - +
183G ILE* 3.2 5.2 - - - -
184G ALA* 3.0 45.3 + - - +
186G ASN* 5.0 8.4 + - - +
202G VAL* 4.6 2.0 - - + +
203G ILE* 1.3 77.7 - - - +
205G MET* 1.3 58.4 + - - +
206G GLU* 5.6 0.2 - - - +
1090I ASN* 4.7 9.3 - - - +
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Residues in contact with MET 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G THR 3.8 1.6 - - - +
23G HIS* 3.6 3.1 + - - -
24G ALA 3.1 40.0 + - - +
26G VAL* 5.2 4.9 - - + -
47G LEU* 3.5 28.7 - - + -
180G VAL* 4.6 2.5 - - + -
183G ILE* 3.3 19.7 - - + -
203G ILE* 4.1 7.5 + - + -
204G GLU* 1.3 74.0 - - - +
206G GLU* 1.3 58.0 - - - +
207G THR* 4.2 21.3 - - + +
211G ILE 5.2 0.4 - - - +
212G ASP 4.7 0.4 - - - +
213G PRO* 3.7 36.8 - - + +
216G ALA* 3.8 23.6 - - + -
217G ILE* 4.4 5.6 - - + +
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Residues in contact with GLU 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G THR* 3.8 6.7 + - - +
23G HIS* 4.0 24.9 - - + +
180G VAL* 4.6 0.2 - - - -
181G GLU* 2.5 42.5 + - + +
182G ARG* 2.6 68.4 + - + +
204G GLU* 6.3 0.2 - - + -
205G MET* 1.3 74.0 - - - +
207G THR* 1.3 60.8 + - - +
1133I LYS* 4.7 11.4 + - - -
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Residues in contact with THR 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G SER 5.3 0.3 + - - -
22G THR* 2.9 36.8 + - - -
179G PRO* 3.1 24.0 - - + +
180G VAL* 3.5 25.6 - - + -
181G GLU* 4.6 5.1 - - - +
205G MET* 4.2 14.7 - - - +
206G GLU* 1.3 80.2 - - - +
208G ASN* 1.3 62.3 + - - +
209G GLY* 3.5 12.5 + - - -
210G THR 4.7 1.1 - - - -
211G ILE* 3.6 24.5 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il